Contacts of the strand formed by residues 111 - 114 (chain G) in PDB entry 2X86
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 111 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72G ILE* 3.7 9.0 - - + -
74G HIS* 3.7 38.1 - + + -
97G SER 4.1 13.2 - - - -
100G LEU* 3.7 20.4 - - + -
101G LEU* 3.8 27.4 - - + -
104G CYS* 3.8 24.5 - - + -
105G LEU* 6.3 0.4 - - + -
109G ILE 4.0 7.0 - - - +
110G PRO* 1.3 73.1 - - - +
112G LEU* 1.3 63.5 + - - +
113G TYR* 3.5 29.4 - + + -
147G PHE* 4.0 14.8 - + - -
161G GLN 3.0 12.7 + - - +
162G ILE* 3.3 7.9 + - + -
163G VAL 2.9 23.7 + - - -
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Residues in contact with LEU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ALA* 4.3 9.4 - - + -
72G ILE 2.9 14.3 + - - +
73G PHE* 3.2 28.4 - - + -
74G HIS* 2.7 31.2 + - - -
75G GLU* 3.7 4.5 - - - +
110G PRO* 4.0 17.9 - - + +
111G PHE* 1.3 79.8 - - - +
113G TYR* 1.3 55.7 + - - +
161G GLN* 4.1 17.3 - - - +
163G VAL* 3.3 13.2 - - + +
165G PHE* 4.2 14.6 - - + -
221G ASN* 4.0 8.7 - - - +
224G PHE* 4.0 14.8 - - + -
225G LEU* 3.9 26.9 - - + +
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G HIS* 3.5 17.9 - + + +
75G GLU* 4.5 4.5 - - - -
97G SER* 5.9 0.2 - - - -
111G PHE* 3.5 36.8 - + + -
112G LEU* 1.3 75.0 - - - +
114G ALA* 1.3 76.8 + - - +
115G SER* 4.1 2.2 - - - -
147G PHE* 3.7 17.5 - + - -
148G ASP* 2.7 29.1 + - - -
151G VAL* 3.4 34.1 - - + +
162G ILE* 4.2 6.7 - - + -
163G VAL 2.7 27.0 + - - +
164G GLY* 3.4 23.2 - - - -
165G PHE* 2.9 31.6 + - - -
232G ILE* 3.7 15.8 - - - +
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Residues in contact with ALA 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G HIS 3.2 10.9 + - - +
75G GLU* 3.7 7.2 - - - +
113G TYR* 1.3 84.7 - - - +
115G SER* 1.3 59.2 + - - +
144G LYS* 3.0 22.0 + - - +
147G PHE* 5.8 0.2 - - - -
165G PHE 3.9 3.4 - - - -
167G TYR* 3.5 15.9 - - + -
400G NAP 3.3 41.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il